Assuming you are talking about web applications from banks and non-tech Fortune 500 in general, it's because many of them are:
* incredibly bloated (and still lack most of the features
that an actual human user would want)
* poorly coded by armies of outsourced programmers
* using over-engineered code built on top of obsolete frameworks
* running on a "homologated" stack, which is often 3 to 7 years out-of-date
(I know because I was partially responsible for some of them, in my dark past.)
Fast Java code that is smartly written is really fast. There are lots of real world Java apps out there that you might not realize are Java --- I've read somewhere that Google Adwords is in Java, for instance.
The problem is, there are lots and lots (and lots) of bad Java developers out there --- it's the "safest language" there is (to learn if you want to make a buck or to hire devs if you want to play it safe as a manager at BigCorp), so you often see badly done outsourced work written in Java. Also, lots of Java code out there lives in non-Agile environments (so it runs on very outdated stacks.)
That being said, if you used a purely modern Java stack (probably some Guice, Wicket, Resin, JDK 7, etc) with super smart people you will be highly performant.
(Note: I haven't done pure real Java dev since the Struts days and Java 1.5, so the tech stack above is just me guessing at what the latest/greatest is.)
